Rooney was left out of the starting XI for the 4-1 Premier League win over Leicester on Saturday after heavy criticism of his recent performances.
Mourinho insisted his decision was based on exploiting Leicester's weaknesses rather than as a reaction to Rooney's form and that he had planned to start the striker in the Europa League on Thursday.
But Rooney only returned to full training on Wednesday after a slight back problem, causing Mourinho to have second thoughts as he seeks to "protect" the England captain.
The United boss said: "Wayne Rooney is selected, I didn't decide yet if I start with him.
"He didn't train yesterday, he did just a little bit of the session on Monday
Today was the first time that he had a training session with the other players and today is the training session where the intensity and the complexity is obviously reduced because we have a game tomorrow.
"So I was completely convinced of playing him tomorrow from the beginning
But with this situation in the last couple of days I'm not sure if I'll do that because, with the situation that you create for him, I think really he can't afford to have a performance that is not really good.
"Because I'm here to protect him and not to put him in difficult situations, I have to analyse if the best thing for him is to start the game if he is not totally ready for it, so I'm going to discuss that with him and the medical staff."
United's performance without Rooney against Leicester only served to increase the spotlight on the 30-year-old's future.
Midfielder Jesse Lingard said of Rooney's absence: " I don't think there was a difference, it's just the mentality on the match day
"Wayne's a top-class professional, top-class player, who's won many things with Man United and he's still got many years to go
He's an inspirational guy and he's a leader
"Obviously against Leicester the manager switched up the team, gave it a different dynamic, and we won the game but, with or without him, we're going to do the best we can as a team, because we are a team and we're going to stick together."
Mourinho confirmed Henrikh Mkhitaryan will again miss out with a thigh problem, although he did train on Wednesday, while full-back Luke Shaw was sent home because of illness
But winger Anthony Martial is fit and striker Zlatan Ibrahimovic will start
There had been rumours the 34-year-old would be rested but, with the international break coming up and Ibrahimovic having retired from Sweden duty, Mourinho sees no problem in him playing on Thursday and at the weekend against Stoke.
Lingard hailed the influence of Ibrahimovic, particularly in the absence of Rooney, saying: " He's been a leader for the team, especially when the captain's not playing
"He's stepped up and he's really led the team
Obviously the young lads look up to him and most of the older lads do as well
We've seen what he's done in his career and obviously he wants to win trophies with Man United
"He talks to the young lads a lot, especially me and Marcus (Rashford), and Paul Pogba, to help us through the games
He's always there for us and he's always there for the team."
United lost their opening Europa League game against Feyenoord two weeks ago, one of three defeats in a row, and Mourinho feels there is now little room for manoeuvre if they are to reach the last 32.
He has been studying little-known Ukrainian side Zorya and said of a victory on Thursday: " It's very important
If we don't win we have four matches and I would say we have to win all the last four matches, which is difficult."
Source : PA
Source: PA